Build/check report for BioC 3.23 - CHECK results for cellmigRation on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.4 LTS)	x86_64	4.6.0 RC (2026-04-17 r89917) -- "Because it was There"	4995
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

CHECK results for cellmigRation on nebbiolo1

To the developers/maintainers of the cellmigRation package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cellmigRation.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: cellmigRation

Version: 1.20.0

Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings cellmigRation_1.20.0.tar.gz

StartedAt: 2026-05-20 22:20:47 -0400 (Wed, 20 May 2026)

EndedAt: 2026-05-20 22:24:49 -0400 (Wed, 20 May 2026)

EllapsedTime: 241.4 seconds

RetCode: 0

Status: OK

CheckDir: cellmigRation.Rcheck

Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:cellmigRation.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings cellmigRation_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/cellmigRation.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-21 02:20:48 UTC
* checking for file ‘cellmigRation/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cellmigRation’ version ‘1.20.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cellmigRation’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... NOTE
Documented arguments not in \usage in Rd file 'fixDA.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM1.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM2.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM3.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM4.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM5.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixFM6.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixID2.Rd':
  ‘TimeInterval’

Documented arguments not in \usage in Rd file 'fixID3.Rd':
  ‘TimeInterval’

Documented arguments not in \usage in Rd file 'fixID4.Rd':
  ‘TimeInterval’

Documented arguments not in \usage in Rd file 'fixMSD.Rd':
  ‘object’

Documented arguments not in \usage in Rd file 'fixPER1.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'fixPER2.Rd':
  ‘x’

Documented arguments not in \usage in Rd file 'innerBondRaster.Rd':
  ‘i’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.23-bioc/meat/cellmigRation.Rcheck/00check.log’
for details.

Installation output

cellmigRation.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL cellmigRation
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘cellmigRation’ ...
** this is package ‘cellmigRation’ version ‘1.20.0’
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cellmigRation)

Tests output

cellmigRation.Rcheck/tests/runTests.Rout


R version 4.6.0 RC (2026-04-17 r89917) -- "Because it was There"
Copyright (C) 2026 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("cellmigRation")


RUNIT TEST PROTOCOL -- Wed May 20 22:22:44 2026 
*********************************************** 
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
cellmigRation RUnit Tests - 7 test functions, 0 errors, 0 failures
Number of test functions: 7 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  3.115   0.250   3.354

Example timings

cellmigRation.Rcheck/cellmigRation-Ex.timings

name	user	system	elapsed
AddDimension	0.000	0.000	0.002
CellMig-class	0.025	0.003	0.028
CellMigPCA	1.465	0.014	1.478
CellMigPCAclust	0.008	0.000	0.008
CellMigPCAclustALL	0.604	0.003	0.607
CellTracker	0.017	0.004	0.021
CellTrackerMainLoop	0.002	0.007	0.008
CentroidArray	0.017	0.003	0.022
CentroidValidation	0.506	0.174	0.680
ComputeTracksStats	0.028	0.006	0.035
DetectRadii	0.002	0.001	0.004
DiAutoCor	1.366	0.058	1.425
DiRatio	0.017	0.001	0.018
DiRatioPlot	0.029	0.008	0.038
EstimateDiameterRange	0.015	0.000	0.015
FMI	0.553	0.165	0.718
FianlizeOptiParams	0.001	0.000	0.000
FilterTrackedCells	0.003	0.000	0.003
FinRes	0.632	0.007	0.641
ForwardMigration	0.934	0.043	0.977
GenAllCombos	0.002	0.001	0.003
LinearConv2	0.019	0.001	0.020
LoadTiff	0.001	0.001	0.001
MSD	1.462	0.045	1.509
MakeHypercube	0.000	0.001	0.002
MigrationStats	0.000	0.001	0.001
NextOdd	0.001	0.000	0.000
NonParallel4OptimizeParams	0.001	0.000	0.001
NonParallelTrackLoop	0	0	0
OptimizeParams	0.015	0.005	0.020
OptimizeParamsMainLoop	0.001	0.008	0.007
Parallel4OptimizeParams	0.000	0.000	0.001
ParallelTrackLoop	0.001	0.000	0.000
PerAndSpeed	0.277	0.007	0.285
PlotTracksSeparately	0.008	0.001	0.009
PostProcessTracking	0	0	0
Prep4OptimizeParams	0.098	0.004	0.102
ThreeConditions	0.014	0.003	0.017
TrackCellsDataset	0.012	0.006	0.018
TrajectoryDataset	0.022	0.001	0.023
ValidateTrackingArgs	0.000	0.001	0.001
VeAutoCor	1.276	0.041	1.318
VisualizeCntr	0.002	0.001	0.002
VisualizeImg	0.002	0.002	0.004
VisualizeStackCentroids	0.054	0.005	0.059
WSADataset	0.006	0.001	0.007
aggregateFR	0.597	0.002	0.599
aggregateTrackedCells	0.022	0.003	0.024
bpass	0.056	0.002	0.058
circshift	0.001	0.000	0.000
cntrd	0.670	0.001	0.671
fixDA	0.001	0.000	0.001
fixExpName	0.000	0.001	0.001
fixFM1	0.000	0.001	0.001
fixFM2	0	0	0
fixFM3	0	0	0
fixFM4	0	0	0
fixFM5	0.001	0.000	0.000
fixFM6	0.000	0.001	0.001
fixID1	0.001	0.000	0.001
fixMSD	0.000	0.000	0.001
fixPER1	0	0	0
fixPER2	0	0	0
fixPER3	0.001	0.000	0.000
getAvailableAggrMetrics	0.837	0.002	0.840
getCellImages	0.195	1.073	1.268
getCellMigSlot	0.255	0.683	0.938
getCellTrackMeta	0.014	0.004	0.018
getCellTrackStats	0.018	0.004	0.021
getCellTracks	0.015	0.004	0.019
getCellsMeta	0.017	0.001	0.018
getCellsStats	0.016	0.004	0.020
getDACtable	1.780	0.023	1.803
getDiRatio	0.017	0.002	0.019
getFMItable	0.425	0.000	0.425
getForMigtable	0.518	0.000	0.518
getImageCentroids	0.018	0.006	0.023
getImageStacks	0.053	0.004	0.057
getMSDtable	3.378	0.015	3.393
getOptimizedParameters	0.016	0.002	0.018
getOptimizedParams	0.019	0.001	0.020
getPerAndSpeed	0.266	0.004	0.270
getPopulationStats	0.014	0.004	0.018
getProcessedImages	0.196	1.089	1.285
getProcessingStatus	0.012	0.006	0.018
getResults	0.607	0.008	0.615
getTracks	0.015	0.004	0.019
getVACtable	0.996	0.000	0.997
initializeTrackParams	0.001	0.000	0.001
innerBondRaster	0.002	0.000	0.002
internalPermutation	0.001	0.001	0.001
matfix	0.001	0.000	0.001
nontrivialBondTracking	0.001	0.000	0.001
pkfnd	0.686	0.003	0.689
plot3DAllTracks	0.074	0.026	0.100
plot3DTracks	0.007	0.002	0.009
plotAllTracks	0.018	0.001	0.019
plotSampleTracks	0.015	0.000	0.015
preProcCellMig	0.007	0.001	0.008
rmPreProcessing	0.083	0.001	0.084
runTrackingPermutation	0.001	0.001	0.002
setAnalyticParams	0.017	0.001	0.017
setCellMigSlot	0.031	0.003	0.034
setCellTracks	0.015	0.003	0.017
setCellsMeta	0.016	0.001	0.017
setExpName	0.020	0.002	0.023
setOptimizedParams	0.015	0.003	0.018
setProcessedImages	0.015	0.003	0.017
setProcessingStatus	0.016	0.001	0.017
setTrackedCellsMeta	0.015	0.003	0.018
setTrackedCentroids	0.014	0.004	0.018
setTrackedPositions	0.013	0.005	0.018
setTrackingStats	0.015	0.004	0.018
sinkAway	0.000	0.001	0.000
subNetworkTracking	0.001	0.000	0.001
track	0.009	0.000	0.009
trackHypercubeBuild	0.000	0.000	0.001
trackSlideProcessing	0.001	0.000	0.001
trackSlideWrapUp	0.000	0.001	0.001
trivialBondRaster	0.002	0.000	0.001
trivialBondTracking	0.000	0.001	0.001
visualizeCellTracks	0.068	0.001	0.069
visualizeTrcks	0.024	0.001	0.025
warnMessage	0.001	0.000	0.000
wsaPreProcessing	0.047	0.001	0.048